RNA polymerase



RNA polymerase (RNAP, DNA primase, dnaG) catalyzes the addition of nucleotides to RNA during transcription. DNA primase (DNAP) is RNAP which catalyzes the synthesis of the RNA primer which complements an ssDNA template and initiates DNA synthesis. dnaG is a bacterial primase.

3D Structures of RNA polymerase
Update June 2011

DNA-dependent RNAP
2y0s – RNAP – Sulfolobus shibata

3q22, 3q23, 3q24 – RNAP + DNA – Enterobacteria phage N4

3p8b – PfRNAP subunit ε’’ + transcription antitermination protein – Pyrococcus furiosus

3qqc - PfRNAP subunits β,ε’’ + transcription antitermination protein

1ryq - PfRNAP subunit ε’’

3lpe - MjRNAP subunit ε’’ + transcription antitermination protein – Methanocaldococcus jannaschii

1go3 – MjRNAP subunit RPB4, RPB7

3aoh, 3aoi - TtRNAP subunits α,β,β’,ω + DNA +RNA + GFH1 – Thermus thermophilus

2o5i, 2o5j - TtRNAP subunits α,β,β’,ω + DNA +RNA

1iw7, 1smy - TtRNAP subunits α,β,β’,ω

1zyr, 2a68, 2a69, 2a6e, 2a6h - TtRNAP subunits α,β,β’,ω + antibiotic

2ppb - TtRNAP subunits α,β,β’,ω + antibiotic + DNA + RNA + substrate analog

2be5 - TtRNAP subunits α,β,β’,ω + σ factor + inhibitor

2cw0 - TtRNAP subunits α,β,β’,ω + σ factor

3dxj, 3eql - TtRNAP subunits α,β,β’,ω + σ factor + antibiotic

1doq - TtRNAP subunit α

3mlq - TtRNAP subunit β + transcription-repair coupling factor

3lti – EcRNAP subunit β fragment – Escherichia coli

3mmp - EcRNAP subunit β + EF-TU

3k4g, 1coo - EcRNAP subunit α

1lb2 - EcRNAP subunit α + DNA + CAP

1xs9 - EcRNAP subunit α + DNA + MARA

1bdf - EcRNAP subunit α (mutant)

3lu0 - EcRNAP subunits α,β,β’,ω – Electron diffraction

3iyd - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + catabolite gene activator + DNA

2l0i – yRNAP C-terminal + RTT103 – yeast – NMR

1a1d – yRNAP subunit RPB8 – NMR

2krc - BsRNAP subunit δ N-terminal – Bacillus subtilis – NMR

3ihq, 1z3e, 3gfk - BsRNAP subunit α +regulatory protein SPX

1qyp – RNAP II C terminal – Thermococcus celer – NMR

3ef0, 3ef1 - SpRNAP II subunit α C terminal – Schizosaccharomyces pombe

3h0g – SpRNAP II

Eukaryotic DNA-dependent RNAP
3o2q, 3o2s – hRNAP II subunit α C-terminal + symplekin – human

1qkl - hRNAP II subunit RPB6

2c35 - hRNAP II subunits RPB4 RPB7 (mutant) – NMR

2f3i - hRNAP II subunits RPB8 RPB17 RPABC3 – NMR

2ghq, 2ght - hRNAP II subunits RPB1 + hRNAP II C terminal

2q5e, 3l0b, 3l0c - hRNAP II C terminal

3pgl - hRNAP II C terminal + inhibitor

2xub, 2xv4 - hRNAP III subunits RPC3

2dk8 – RNAP III RPC34 domain - mouse – NMR

2dk5 – hRNAP III winged helix domain (mutant) – NMR

2yu3 - hRNAP III winged helix domain

3nff, 3nfg, 3nfh, 3nfi – RNAP I fragments (mutant) – Candida glabrata

2rf4 - yRNAP I subunit RPA4

1i6h - yRNAP II + DNA

1nik, 1nt9, 1wcm, 2b8k, 3fki, 3qt1, 1i3q, 1i50, 1dzf – yRNAP II

1y14 - yRNAP II subunits RPB4 RPB7

1pqv, 1y1v - yRNAP II + TFIIS

1y1y - yRNAP II + TFIIS + DNA +RNA

2vum - yRNAP II + inhibitor + DNA + RNA

3cqz, 1k83 - yRNAP II + inhibitor

1r5u, 3k7a, 3k1f - yRNAP II + TFIIB

1r9s, 2ja5, 2ja6, 2ja7, 2ja8, 2nvq, 2nvt, 2nvx, 2nvy, 2nvz, 3gtg, 3gtj, 3gtk, 3gtl, 3gtm, 3gto, 3gtp, 3gtq, 3hou, 3hov, 3how, 3hox, 3hoy, 3hoz, 3po2, 3po3, 3m3y, 3m4o - yRNAP II + RNA + DNA

1y1w, 1y77, 2r7z, 2r92, 2r93, 3h3v - yRNAP II + RNA

1twa, 1twc, 1twf, 1twg, 1twh - yRNAP II + nucleotide

2b63 - yRNAP II + nucleotide + RNA

2e2i, 2e2j - yRNAP II + nucleotide + DNA

2yu9, 3i4m, 3i4n - yRNAP II + nucleotide + DNA + RNA

2ckz - yRNAP III

1ef4 – MtRNAP subunit RPB10 – Methanothermobacter thermautotrophicus

1eik - MtRNAP subunit RPB5 – NMR

Prokaryotic DNA-dependent RNAP
1hqm – TaRNAP subunits α,β,β’,ω − Thermus aquaticus

2gho - TaRNAP subunits α,β,β’

1i6v, 1ynj, 1ynn - TaRNAP subunits α,β,β’,ω + antibiotic

1l9u - TaRNAP subunits α,β,β’,ω + σ factor

1l9z - TaRNAP subunits α,β,β’,ω + σ factor + DNA

2auj, 2auk - TaRNAP subunit β’

1xpp – RNAP subunit L – Thermoplasma acidophilum

2jzb – RNAP subunit α + NUSA transcription elongation factor – Yersinia pseudotuberculosis

2waq, 2wb1 – RNAP – Sulfolobus shibata

3e7h – RNAP subunit β – Vibrio cholerae

RNA-dependent RNAP
3phu, 1khv, 1khw – HfRNAP L RNA-directed – Hemorrhagic fever virus

3phw, 2pt2, 3pt2 – HfRNAP + ubiquitin

3phx – HfRNAP + ISG15

3pse - HfRNAP + ISG15 (mutant)

2xwh, 2xxd, 2xhu, 2xhw, 3i5k, 1c2p, 1csj, 1quv, 1yuy, 1yv2, 1yvx, 1yvz, 3gsz – HvRNAP NS5B domain – Hepatitis virus

2xym, 2xhv, 2xi2 - HvRNAP NS5B domain (mutant)

2xwy, 3mf5, 3hkw, 3hky, 3lkh, 3gnv, 3gnw, 3h98, 3g86, 3h59, 1nhu, 1nhv, 2brk, 2brl, 2gc8, 2giq, 2gir, 2hai, 2hwh, 2hwi, 2i1r, 2ijn, 2jc0, 2jc1, 2qe2, 2qe5, 2wcx, 2who, 3ciz, 3cj0, 3cj2, 3cj3, 3cj4, 3cj5, 3cso, 3cvk, 3fqk, 3fql, 3gol, 3h5s, 3h5u, 3q0z, 3qgd, 3qge, 3qgf, 3qgg, 3qgh, 3qgi - HvRNAP NS5B domain + inhibitor

3gyn, 1os5, 3br9, 3bsa, 3bsc, 3cde, 3co9, 3cwj, 3d28, 3d5m, 3e51, 3frz, 3igv - HvRNAP NS5B domain (mutant) + inhibitor

2wrm – HvRNAP NS5B domain

2xi3 - HvRNAP NS5B domain (mutant) + nucleotide

1gx5, 1gx6 - HvRNAP catalytic domain + nucleotide

3ol6, 2jlg – PoRNAP (mutant) + RNA – Poliovirus

1tql, 2ijd, 2ijf - PoRNAP (mutant)

3ol7, 3ol8, 3ol9, 3ola, 3olb - PoRNAP (mutant) + RNA + nucleotide

2xi5, 2xi7 – RNAP L N-terminal – Bunyavirus

3jsb – RNAP (mutant) – Lymphocytic choriomengitis virus

2wk4, 2uut, 2uuw – SvRNAP (mutant) – Sapporo virus

2ckw - SvRNAP residues 1135-1649

3klv, 3kmq, 3kms, 3kna – FmRNAP (mutant) + RNA – Foot-and-mouth virus

3koa - FmRNAP (mutant) + RNA + nucleotide

1wne – FmRNAP + RNA 2e9r, 2e9t, 2e9z, 2ec0 - FmRNAP + RNA + inhibitor 2d7s, 2f83 – FmRNAP + VPG protein 3hw3, 3hw6 - IvRNAP subunit P2 (mutant) – Influenza virus

2znl - IvRNAP subunit P1 + polymerase acidic protein

2ztt, 3a1g - IvRNAP subunit P1 + polymerase basic protein

2w69 - IvRNAP subunit P2

3hw5 - IvRNAP subunit P2 (mutant) + AMP

2gmo, 3cw4 - IvRNAP subunit P3

2vqz - IvRNAP subunit P3 CAP-binding domain

2vy6 - IvRNAP subunit P3 627- and NLS domains

2vy7 - IvRNAP subunit P3 627-domain

2vy8 - IvRNAP subunit P3 627-domain (mutant)

1hhs – P6RNAP – Bacteriophage φ-6

2jl9, 2jlf – P6RNAP (mutant)

1uvi, 1uvl, 1uvm, 1uvn – P6RNAP + RNA

2po4 – N4RNAP polymerase domain – Bacteriophage N4

3c2p, 3c3l, 3c46, 3q0a - N4RNAP polymerase domain + promoter DNA

1l9k – DevRNAP N terminal – Dengue virus

2j7u - DevRNAP polymerase domain

1oks – RNAP α subunit – Measles virus

1r4g - RNAP α subunit – Sendai virus – NMR

1s48, 1s49, 1s4f – DvRNAP residues 71-679 – Diarrhea virus

2cjq - DvRNAP polymerase domain

1sh0, 1sh2, 1sh3 - NvRNAP C terminal – Norwalk virus

3bsn, 3bso, 3h5x, 3h5y - NvRNAP + RNA + nucleotide

1vyi - RNAP α subunit C terminal – Rabies virus

2hcn, 2hcs, 2hfz – RNAP polymerase domain – West Nile virus

2pgg, 2pus – RNAP – Bursal disease virus

2r7o, 2r7q – SrRNAP – Simian rotavirus

2r7r, 2r7s, 2r7t, 2r7u, 2r7v, 2r7w, 2r7x – SrRNAP + RNA

3cdu – CvRNAP + POP – Coxsakievirus

3ddk - CvRNAP

3cdw - CvRNAP + POP + VPG

3eva, 3evb, 3evc, 3evd, 3eve, 3evf, 3evg – RNAP N terminal + nucleotide – Yellow fever virus

2j7n, 2j7o – RNAP residues 381-1402 – Neurospora crassa

DNA primase
3l9q – hDNAP large subunit

3lgb - yDNAP large subunit

3m1m – DNAP RNA polymerase domain – Sulfolobus islandicus

1zt2, 2pa8, 2pmz, 3hkz - DNAP small + large subunit – Sulfolobus solfataricus

2au3 – DNAP zinc-binding and RNA polymerase domains – Aquifex aeolicus

1v33 - PhDNAP small subunit – Pyrocuccus horikoshii

1v34 - PhDNAP small subunit + nucleotide

1g71 - PfDNAP small subunit

1q57 – T7DNAP/helicase (mutant) – Enterobacteria phage T7

1nui – T7DNAP/helicase primase fragment (mutant)

1cr0 - T7DNAP/helicase helicase domain

1cr1, 1cr2, 1cr4 - T7DNAP/helicase helicase domain + nucleotide

Bacterial primase
2r6c – dnaG helicase binding domain + helicase – Bacillus stearothermophilus

2r6a - GsdnaG helicase binding domain + helicase – Geobacillus stearothermophilus

1d0q - GsDNAP zinc-binding domain

1z8s - GsdnaG dnaB binding domain - NMR

2haj - EcdnaG catalytic domain - NMR

3b39 – EcdnaG catalytic domain + DNA

1t3w – EcdnaG C-terminal

1eqn, 1dd9, 1dde – EcdnaG catalytic core

RNA polymerase from Bacteriophage T7
4rnp – T7RNAP

1aro – T7RNAP + T7 lysozyme

1cez, 1h38, 1qln, 2pi4, 2pi5 - T7RNAP + DNA

1msw, 1s0v, 1s76, 1s77, 3e2e, 3e3j - T7RNAP + DNA + RNA

Poly(A) RNA polymerase
3pq1 – hPAP (mutant)